greg,
By default Eclipse “cleans” its output directory when building, this means basically “deleting everything in the output folder”. Your properties file should actually go into your source tree in the root of it, then Eclipse will copy it over into the output dir for you when it builds.
If you absolutely have to have it in your classes folder (not suggested at all, because you shouldn’t have this in source control anyway) you can turn off the auto cleaning under the Window > Preferences > Java > Compiler > (last tab) settings, but I believe when you rebuild the project or “clean it” it will just erase the file anyway again… so its best you don’t put it there.